Very simple oversight and result-

When unlocking "religious tolerance", I picked "religious hostility", which unlocked "unbelievers".

Ideological proximity then forced me to revoke those civics.

After that, I switched "religious tolerance" to "open minded" which unlocked "religious minorities"

So I had both brances of the "religious tolderance" choice unlocked at once.

To boot, this also broke "I come Bearing Steam" by giving the options unlocked by both civics at the same time.